De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.)

Pomegranate (Punica granatum L.) belongs to Punicaceae, and is valued for its social, ecological, economic, and aesthetic values, as well as more recently for its health benefits. The 'Tunisia' variety has softer seeds and big arils that are easily swallowed. It is a widely popular fruit;...

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Published in:	PloS one 2017-06, Vol.12 (6), p.e0178809-e0178809
Main Authors:	Xue, Hui, Cao, Shangyin, Li, Haoxian, Zhang, Jie, Niu, Juan, Chen, Lina, Zhang, Fuhong, Zhao, Diguang
Format:	Article
Language:	eng
Subjects:	Acetylcysteine Apoptosis Assembly Bioinformatics Biology and Life Sciences Biosynthesis Cell death Cellulose Cloning Coding Computational Biology Cultivars Data acquisition Data bases Ecology Economics Enrichment Evolution Flavonoids Fruit Fruit seeds Fruits Gene expression Gene Expression Profiling - methods Gene Expression Regulation, Plant - genetics Genes Genomes Health Laccase Lignin Mathematical models Metabolism Molecular modelling Mortality Peroxidase Physical Sciences Physiological aspects Polymerase chain reaction Pomegranate Pomegranates Proteins Punica granatum Punicaceae Punicaceae - genetics Research and analysis methods Reverse Transcriptase Polymerase Chain Reaction Seeds Social behavior Transcription factors
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Summary:	Pomegranate (Punica granatum L.) belongs to Punicaceae, and is valued for its social, ecological, economic, and aesthetic values, as well as more recently for its health benefits. The 'Tunisia' variety has softer seeds and big arils that are easily swallowed. It is a widely popular fruit; however, the molecular mechanisms of the formation of hard and soft seeds is not yet clear. We conducted a de novo assembly of the seed transcriptome in P. granatum L. and revealed differential gene expression between the soft-seed and hard-seed pomegranate varieties. A total of 35.1 Gb of data were acquired in this study, including 280,881,106 raw reads. Additionally, de novo transcriptome assembly generated 132,287 transcripts and 105,743 representative unigenes; approximately 13,805 unigenes (37.7%) were longer than 1,000 bp. Using bioinformatics annotation libraries, a total of 76,806 unigenes were annotated and, among the high-quality reads, 72.63% had at least one significant match to an existing gene model. Gene expression and differentially expressed genes were analyzed. The seed formation of the two pomegranate cultivars involves lignin biosynthesis and metabolism, including some genes encoding laccase and peroxidase, WRKY, MYB, and NAC transcription factors. In the hard-seed pomegranate, lignin-related genes and cellulose synthesis-related genes were highly expressed; in soft-seed pomegranates, expression of genes related to flavonoids and programmed cell death was slightly higher. We validated selection of the identified genes using qRT-PCR. This is the first transcriptome analysis of P. granatum L. This transcription sequencing greatly enriched the pomegranate molecular database, and the high-quality SSRs generated in this study will aid the gene cloning from pomegranate in the future. It provides important insights into the molecular mechanisms underlying the formation of soft seeds in pomegranate.
ISSN:	1932-6203 1932-6203